hi,

... the obvious thing to try is to toggle USE_FSETOWNCTTY in
xntp/include/config.h to stop xntpd/ntp_io.c from attempting the
TIOCSCTTY ioctl.  

If that breaks the subsequen FSETOWN fcntl() then I guess you should
send a PR.

Failing that, you could try using /dev/dty0 instead...

(PS: if you are interested in debugging the PPS_SYNC code please
email me.)